r4443 - in /branches/N_state_model/test_suite/system_tests: n_state_model.py scripts/5_state_xz.py -- January 07, 2008 - 17:46

Author: bugman
Date: Mon Jan  7 17:46:57 2008
New Revision: 4443

URL: http://svn.gna.org/viewcvs/relax?rev=4443&view=rev
Log:
Created a script containing the commands used in the N-state model system 
test.

The system test tries to execute the script.  Work still needs to be done 
here though.


Added:
    branches/N_state_model/test_suite/system_tests/scripts/5_state_xz.py
Modified:
    branches/N_state_model/test_suite/system_tests/n_state_model.py

Modified: branches/N_state_model/test_suite/system_tests/n_state_model.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/system_tests/n_state_model.py?rev=4443&r1=4442&r2=4443&view=diff
==============================================================================
--- branches/N_state_model/test_suite/system_tests/n_state_model.py (original)
+++ branches/N_state_model/test_suite/system_tests/n_state_model.py Mon Jan  
7 17:46:57 2008
@@ -49,6 +49,11 @@
             State 5:    {0, -pi/4, 0}
         """
 
+        # Execute the script '5_state_xz.py'.
+        
self.relax.interpreter.script('test_suite/system_tests/scripts/5_state_xz.py')
+
+        return
+
         # Create the data pipe.
         self.relax.interpreter._Pipe.create('C domain', 'N-state')
 

Added: branches/N_state_model/test_suite/system_tests/scripts/5_state_xz.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/system_tests/scripts/5_state_xz.py?rev=4443&view=auto
==============================================================================
--- branches/N_state_model/test_suite/system_tests/scripts/5_state_xz.py 
(added)
+++ branches/N_state_model/test_suite/system_tests/scripts/5_state_xz.py Mon 
Jan  7 17:46:57 2008
@@ -1,0 +1,55 @@
+"""A 5-state model in the xz-plane (no pivotting of alpha).
+
+The 5 states correspond to the Euler angles (z-y-z notation):
+    State 1:    {0, pi/4, 0}
+    State 2:    {0, pi/8, 0}
+    State 3:    {0, 0, 0}
+    State 4:    {0, -pi/8, 0}
+    State 5:    {0, -pi/4, 0}
+"""
+
+# Create the data pipe.
+pipe.create('C domain', 'N-state')
+
+# Load the C-terminal alignment tensors..
+align_tensor.init(tensor='chi1', params=(-1/2., -1/2.,  0.,   0.,     0.))
+align_tensor.init(tensor='chi2', params=(-1/8., -7/8.,  0.,   0.,     0.))
+align_tensor.init(tensor='chi3', params=(-1/8.,  1/16., 0.,   0.,    
-15/16.))
+align_tensor.init(tensor='chi4', params=(7/16., -7/8.,  0.,   9/16.,  0.))
+align_tensor.init(tensor='chi5', params=(-1/2., -1/2.,  3/8., 0.,     0.))
+
+# Calculate the singular values.
+align_tensor.svd(basis_set=0)
+align_tensor.svd(basis_set=1)
+
+# Calculate the angles between the matrices.
+align_tensor.matrix_angles(basis_set=0)
+align_tensor.matrix_angles(basis_set=1)
+
+
+# Create the data pipe.
+pipe.create('N domain', 'N-state')
+
+# Load the N-terminal alignment tensors.
+align_tensor.init(tensor='chi1', params=(1/4.,   -1/2.,   0.,              
3/4.,   0.))
+align_tensor.init(tensor='chi2', params=(7/16.,  -7/8.,   0.,              
9/16.,  0.))
+align_tensor.init(tensor='chi3', params=(-1/32.,  1/16., -15/(16*sqrt(2)), 
3/32., -15/(16*sqrt(2))))
+align_tensor.init(tensor='chi4', params=(1.,     -7/8.,   0.,              
0.,     0.))
+align_tensor.init(tensor='chi5', params=(1/4.,   -1/2.,   3/(8*sqrt(2)),   
3/4.,  -3/(8*sqrt(2))))
+
+# Calculate the singular values.
+align_tensor.svd(basis_set=0)
+align_tensor.svd(basis_set=1)
+
+# Calculate the angles between the matrices.
+align_tensor.matrix_angles(basis_set=0)
+align_tensor.matrix_angles(basis_set=1)
+
+# Grid search.
+minimisation.grid_search(inc=11)
+
+# Minimise.
+minimisation.minimise('simplex')
+
+# Finish.
+#results.write(file='devnull', force=1)